X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=8913a322187e8df056962543d134af1573f0056d;hb=91e9ddff22dd9406d8784b8a91f03d7b94b4a180;hp=a7963df5b4f1f8eeb63e4a4a79086310cf032828;hpb=32254db18cc678b675db8d0cd72a525a6034bf01;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index a7963df..8913a32 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -1,21 +1,24 @@
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
Release History
@@ -33,338 +36,405 @@
Issues Resolved
+
+ |
+
+
+ General
+ Application
+
+ - Update Jalview project format:
+
+
+
+ |
+
+ Application
+ Applet
+ Other
+
+ |
+
+
+ |
+
+
+ General
+
+ - Internationalisation of user interface (usually called
+ i18n support) and translation for Spanish locale
+ - Define/Undefine group on current selection with
+ Ctrl-G/Shift Ctrl-G
+ - Improved group creation/removal options in
+ alignment/sequence Popup menu
+ - Sensible precision for symbol distribution percentages
+ shown in logo tooltip.
+ - Annotation panel height set according to amount of
+ annotation when alignment first opened
+ Application
+
+ - Interactive consensus RNA secondary structure prediction
+ VIENNA RNAAliFold JABA 2.1 service
+ - Select columns containing particular features from Feature
+ Settings dialog
+ - View all 'representative' PDB structures for selected
+ sequences
+ - Update Jalview project format:
+
+ - New file extension for Jalview projects '.jvp'
+ - Preserve sequence and annotation dataset (to store
+ secondary structure annotation,etc)
+ - Per group and alignment annotation and RNA helix
+ colouring
+
+
+ - New similarity measures for PCA and Tree calculation
+ (PAM250)
+ - Experimental support for retrieval and viewing of flanking
+ regions for an alignment
+
+ |
+
+ Application
+
+ - logo keeps spinning and status remains at queued or
+ running after job is cancelled
+ - cannot export features from alignments imported from
+ Jalview/VAMSAS projects
+ - Buggy slider for web service parameters that take float
+ values
+ - Newly created RNA secondary structure line doesn't have
+ 'display all symbols' flag set
+ - T-COFFEE alignment score shading scheme and other
+ annotation shading not saved in jalview project
+ - Local file cannot be loaded in freshly downloaded Jalview
+ - Jalview icon not shown on dock in Mountain Lion/Webstart
+ - Load file from desktop file browser fails
+ - Occasional NPE thrown when calculating large trees
+ - Cannot reorder or slide sequences after dragging an
+ alignment onto desktop
+ - Colour by annotation dialog throws NPE after using
+ 'extract scores' function
+ - Loading/cut'n'pasting an empty file leads to a grey
+ alignment window
+ - Disorder thresholds rendered incorrectly after performing
+ IUPred disorder prediction
+ - Multiple group annotated consensus rows shown when
+ changing 'normalise logo' display setting
+ - Find shows blank dialog after 'finished searching' if
+ nothing matches query
+ - Null Pointer Exceptions raised when sorting by feature
+ with lots of groups
+
+ - Errors in Jmol console when structures in alignment don't
+ overlap
+
+ - Not all working JABAWS services are shown in Jalview's
+ menu
+ - JAVAWS version of jalview fails to launch with 'invalid
+ literal/length code'
+ - Annotation/RNA Helix colourschemes cannot be applied to
+ alignment with groups (actually fixed in 2.8.0b1)
+ - RNA Helices and T-Coffee Scores available as default colourscheme
+
+ Applet
+
+ - Remove group option is shown even when selection is not a
+ group
+ - Apply to all groups ticked but colourscheme changes don't
+ affect groups
+ - Documented RNA Helices and T-Coffee Scores as valid colourscheme name
+ - Annotation labels drawn on sequence IDs when Annotation panel is not displayed
+ - Increased font size for dropdown menus on OSX and embedded windows
+ Other
+
+ - Consensus sequence for alignments/groups with a single
+ sequence were not calculated
+ - annotation files that contain only groups imported as
+ annotation and junk sequences
+ - Fasta files with sequences containing '*' incorrectly
+ recognised as PFAM or BLC
+ - conservation/PID slider apply all groups option doesn't
+ affect background (2.8.0b1)
+
+ - redundancy highlighting is erratic at 0% and 100%
+ - Remove gapped columns fails for sequences with ragged
+ trailing gaps
+ - AMSA annotation row with leading spaces is not registered
+ correctly on import
+ - Jalview crashes when selecting PCA analysis for certain
+ alignments
+ - Opening the colour by annotation dialog for an existing
+ annotation based 'use original colours' colourscheme loses
+ original colours setting
+
+ |
+
+
+ |
+ |
+
+
+ - Trusted certificates for JalviewLite applet and
+ Jalview Desktop application
Certificate was donated by
+ Certum to the Jalview
+ open source project).
+
+ - Jalview SRS links replaced by Uniprot and EBI-search
+
+ - Output in Stockholm format
+ - Allow import of data from gzipped files
+ - Export/import group and sequence associated line
+ graph thresholds
+ - Nucleotide substitution matrix that supports RNA and
+ ambiguity codes
+ - Allow disorder predictions to be made on the current
+ selection (or visible selection) in the same way that JPred
+ works
+ - Groovy scripting for headless jalview operation
+ Other improvements
+
+ - Upgrade desktop installer to InstallAnywhere 2013
+ - COMBINE statement uses current SEQUENCE_REF and
+ GROUP_REF scope to group annotation rows
+ - Support '' style escaping of quotes in Newick
+ files
+ - Group options for JABAWS service by command line name
+ - Empty tooltip shown for JABA service options with a
+ link but no description
+ - Select primary source when selecting authority in
+ database fetcher GUI
+ - Add .mfa to FASTA file extensions recognised by
+ Jalview
+ - Annotation label tooltip text wrap
+
+ |
+
+
+ - Slow scrolling when lots of annotation rows are
+ displayed
+ - Lots of NPE (and slowness) after creating RNA
+ secondary structure annotation line
+ - Sequence database accessions not imported when
+ fetching alignments from Rfam
+ - Incorrect SHMR submission for sequences with
+ identical IDs
+ - View all structures does not always superpose
+ structures
+ - Option widgets in service parameters not updated to
+ reflect user or preset settings
+ - Null pointer exceptions for some services without
+ presets or adjustable parameters
+ - Discover PDB IDs entry in structure menu doesn't
+ discover PDB xRefs
+ - Exception encountered while trying to retrieve
+ features with DAS
+ - Lowest value in annotation row isn't coloured
+ when colour by annotation (per sequence) is coloured
+ - Keyboard mode P jumps to start of gapped region when
+ residue follows a gap
+ - Jalview appears to hang importing an alignment with
+ Wrap as default or after enabling Wrap
+ - 'Right click to add annotations' message
+ shown in wrap mode when no annotations present
+ - Disorder predictions fail with NPE if no automatic
+ annotation already exists on alignment
+ - oninit javascript function should be called after
+ initialisation completes
+ - Remove redundancy after disorder prediction corrupts
+ alignment window display
+ - Example annotation file in documentation is invalid
+ - Grouped line graph annotation rows are not exported
+ to annotation file
+ - Multi-harmony analysis cannot be run when only two
+ groups created
+ - Cannot create multiple groups of line graphs with
+ several 'combine' statements in annotation file
+ - Pressing return several times causes Number Format
+ exceptions in keyboard mode
+ - Multi-harmony (SHMMR) method doesn't submit
+ correct partitions for input data
+ - Translation from DNA to Amino Acids fails
+ - Jalview fail to load newick tree with quoted label
+ - --headless flag isn't understood
+ - ClassCastException when generating EPS in headless
+ mode
+ - Adjusting sequence-associated shading threshold only
+ changes one row's threshold
+ - Preferences and Feature settings panel panel
+ doesn't open
+ - hide consensus histogram also hides conservation and
+ quality histograms
+
+ |
+
- 2.8 08/11/2012
+ 2.8 12/11/2012
|
Application
- Support for JABAWS 2.0 Services (AACon alignment
- conservation, protein disorder and Clustal Omega)
-
-
-
-
- JABAWS
- server status indicator in Web Services preferences
-
-
- VARNA
- (http://varna.lri.fr) viewer for RNA structures in Jalview
- alignment window
-
-
- Updated
- jalview build and deploy framework for OSX mountain lion, windows
- 7, and 8
+ - Support for JABAWS 2.0 Services (AACon alignment
+ conservation, protein disorder and Clustal Omega)
+ - JABAWS server status indicator in Web Services preferences
+ - VARNA (http://varna.lri.fr) viewer for RNA structures in
+ Jalview alignment window
+ - Updated Jalview build and deploy framework for OSX mountain
+ lion, windows 7, and 8
- Nucleotide substitution matrix for PCA that supports RNA
- and ambiguity codes
-
+ and ambiguity codes
Improved sequence database retrieval GUI
- Support fetching and database reference look up against
- multiple DAS sources (Fetch all from in 'fetch db refs')
-
+ Support fetching and database reference look up against
+ multiple DAS sources (Fetch all from in 'fetch db refs')
Jalview project improvements
- -
- Store
- and retrieve the 'belowAlignment' flag for annotation
-
- -
- calcId
- attribute to group annotation rows on the alignment
-
- -
- Store
- AACon calculation settings for a view in Jalview project
-
+ - Store and retrieve the 'belowAlignment' flag for
+ annotation
+ - calcId attribute to group annotation rows on the
+ alignment
+ - Store AACon calculation settings for a view in Jalview
+ project
-
- horizontal
- scrolling gesture support
-
- Visual progress indicator when PCA calculation is running
-
- Simpler JABA web services menus
-
-
- visual
- indication that web service results are still being retrieved from
- server
-
-
- Serialise
- the dialogs that are shown when jalview starts up for first time
-
-
- Jalview
- user agent string for interacting with HTTP services
-
-
- DAS
- 1.6 and DAS 2.0 source support using new JDAS client library
-
+ horizontal scrolling gesture support
+ Visual progress indicator when PCA calculation is running
+ Simpler JABA web services menus
+ visual indication that web service results are still being
+ retrieved from server
+ Serialise the dialogs that are shown when Jalview starts up
+ for first time
+ Jalview user agent string for interacting with HTTP
+ services
+ DAS 1.6 and DAS 2.0 source support using new JDAS client
+ library
+ Examples directory and Groovy library included in
+ InstallAnywhere distribution
Applet
- -
- RNA
- alignment and secondary structure annotation visualization applet
- example
-
+ - RNA alignment and secondary structure annotation
+ visualization applet example
General
- -
- Normalise
- option for consensus sequence logo
-
- -
- Reset
- button in PCA window to return dimensions to defaults
-
- -
- Allow
- seqspace or Jalview variant of alignment PCA calculation
-
- -
- PCA
- with either nucleic acid and protein substitution matrices
-
-
- Allow
- windows containing HTML reports to be exported in HTML
-
- -
- Interactive
- display and editing of RNA secondary structure contacts
-
+ - Normalise option for consensus sequence logo
+ - Reset button in PCA window to return dimensions to
+ defaults
+ - Allow seqspace or Jalview variant of alignment PCA
+ calculation
+ - PCA with either nucleic acid and protein substitution
+ matrices
+
- Allow windows containing HTML reports to be exported in
+ HTML
+ - Interactive display and editing of RNA secondary structure
+ contacts
- RNA Helix Alignment Colouring
- RNA base pair logo consensus
- -
- Parse
- sequence associated secondary structure information in Stockholm
- files
-
- -
- HTML
- Export database accessions and annotation information presented in
- tooltip for sequences
-
- -
- Import
- secondary structure from LOCARNA clustalw style RNA alignment
- files
-
- -
- import
- and visualise T-COFFEE quality scores for an alignment
-
- -
- 'colour
- by annotation' per sequence option to shade each sequence
- according to its associated alignment annotation
-
- -
- New
- Jalview Logo
-
+ - Parse sequence associated secondary structure information
+ in Stockholm files
+ - HTML Export database accessions and annotation information
+ presented in tooltip for sequences
+ - Import secondary structure from LOCARNA clustalw style RNA
+ alignment files
+ - import and visualise T-COFFEE quality scores for an
+ alignment
+ - 'colour by annotation' per sequence option to
+ shade each sequence according to its associated alignment
+ annotation
+ - New Jalview Logo
Documentation and Development
- -
- documentation
- for score matrices used in Jalview
-
+ - documentation for score matrices used in Jalview
- New Website!
|
Application
- PDB, Unprot and EMBL (ENA) databases retrieved via
- wsdbfetch REST service
-
- -
-
- Stop
- windows being moved outside desktop on OSX
-
- -
- Filetype
- associations not installed for webstart launch
-
- -
- Jalview
- does not always retrieve progress of a JABAWS job execution in
- full once it is complete
-
- -
- revise
- SHMR RSBS definition to ensure alignment is uploaded via ali_file
- parameter
-
- -
- Jalview
- 2.7 is incompatible with Jmol-12.2.2
-
- -
- View
- all structures superposed fails with exception
-
- -
- Jnet
- job queues forever if a very short sequence is submitted for
- prediction
-
- -
- Cut
- and paste menu not opened when mouse clicked on desktop window
-
- -
- Putting
- fractional value into integer text box in alignment parameter
- dialog causes jalview to hang
-
- -
- Structure
- view highlighting doesn't work on windows 7
-
- -
- View
- all structures fails with exception shown in structure view
-
- -
- Characters
- in filename associated with PDBEntry not escaped in a platform
- independent way
-
- -
- Jalview
- desktop fails to launch with exception when using proxy
-
- -
- Tree
- calculation reports 'you must have 2 or more sequences
- selected' when selection is empty
-
- -
- Jalview
- desktop fails to launch with jar signature failure when java web
- start temporary file caching is disabled
-
- -
- DAS
- Sequence retrieval with range qualification results in sequence
- xref which includes range qualification
-
- -
- Errors
- during processing of command line arguments cause progress bar
- (JAL-898) to be removed
-
- -
- Replace
- comma for semi-colon option not disabled for DAS sources in
- sequence fetcher
-
- -
- Cannot
- close news reader when JABAWS server warning dialog is shown
-
- -
- Option
- widgets not updated to reflect user settings
-
- -
- Edited
- sequence not submitted to web service
-
- -
- Jalview
- 2.7 Webstart does not launch on mountain lion
-
- -
- InstallAnywhere
- installer doesn't unpack and run on OSX Mountain Lion
-
- -
- Annotation
- panel not given a scroll bar when sequences with alignment
- annotation are pasted into the alignment
-
- -
- Sequence
- associated annotation rows not associated when loaded from jalview
- project
-
- -
- Browser
- launch fails with NPE on java 1.7
-
- -
- JABAWS
- alignment marked as finished when job was cancelled or job failed
- due to invalid input
-
- -
- NPE
- with v2.7 example when clicking on Tree associated with all views
-
- -
- Exceptions
- when copy/paste sequences with grouped annotation rows to new
- window
+ wsdbfetch REST service
+ - Stop windows being moved outside desktop on OSX
+ - Filetype associations not installed for webstart launch
+ - Jalview does not always retrieve progress of a JABAWS job
+ execution in full once it is complete
+ - revise SHMR RSBS definition to ensure alignment is
+ uploaded via ali_file parameter
+ - Jalview 2.7 is incompatible with Jmol-12.2.2
+ - View all structures superposed fails with exception
+ - Jnet job queues forever if a very short sequence is
+ submitted for prediction
+ - Cut and paste menu not opened when mouse clicked on
+ desktop window
+ - Putting fractional value into integer text box in
+ alignment parameter dialog causes Jalview to hang
+ - Structure view highlighting doesn't work on windows 7
+ - View all structures fails with exception shown in
+ structure view
+ - Characters in filename associated with PDBEntry not
+ escaped in a platform independent way
+ - Jalview desktop fails to launch with exception when using
+ proxy
+ - Tree calculation reports 'you must have 2 or more
+ sequences selected' when selection is empty
+ - Jalview desktop fails to launch with jar signature failure
+ when java web start temporary file caching is disabled
+ - DAS Sequence retrieval with range qualification results in
+ sequence xref which includes range qualification
+ - Errors during processing of command line arguments cause
+ progress bar (JAL-898) to be removed
+ - Replace comma for semi-colon option not disabled for DAS
+ sources in sequence fetcher
+ - Cannot close news reader when JABAWS server warning dialog
+ is shown
+ - Option widgets not updated to reflect user settings
+ - Edited sequence not submitted to web service
+ - Jalview 2.7 Webstart does not launch on mountain lion
+ - InstallAnywhere installer doesn't unpack and run on
+ OSX Mountain Lion
+ - Annotation panel not given a scroll bar when sequences
+ with alignment annotation are pasted into the alignment
+ - Sequence associated annotation rows not associated when
+ loaded from Jalview project
+ - Browser launch fails with NPE on java 1.7
+ - JABAWS alignment marked as finished when job was cancelled
+ or job failed due to invalid input
+ - NPE with v2.7 example when clicking on Tree associated
+ with all views
+ - Exceptions when copy/paste sequences with grouped
+ annotation rows to new window
Applet
- -
- Sequence
- features are momentarily displayed before they are hidden using
- hidefeaturegroups applet parameter
-
- -
- loading
- features via javascript API automatically enables feature display
-
- -
- scrollToColumnIn
- javascript API method doesn't work
-
+ - Sequence features are momentarily displayed before they
+ are hidden using hidefeaturegroups applet parameter
+ - loading features via javascript API automatically enables
+ feature display
+ - scrollToColumnIn javascript API method doesn't work
General
- -
- Redundancy
- removal fails for rna alignment
-
- -
- PCA
- calculation fails when sequence has been selected and then
- deselected
-
- -
- PCA
- window shows grey box when first opened on OSX
-
- -
- Letters
- coloured pink in sequence logo when alignment coloured with
- clustalx
-
- -
- Choosing
- fonts without letter symbols defined causes exceptions and redraw
- errors
-
- -
- Initial
- PCA plot view is not same as manually reconfigured view
-
- -
- Grouped
- annotation graph label has incorrect line colour
-
- -
- Grouped
- annotation graph label display is corrupted for lots of labels
-
+ - Redundancy removal fails for rna alignment
+ - PCA calculation fails when sequence has been selected and
+ then deselected
+ - PCA window shows grey box when first opened on OSX
+ - Letters coloured pink in sequence logo when alignment
+ coloured with clustalx
+ - Choosing fonts without letter symbols defined causes
+ exceptions and redraw errors
+ - Initial PCA plot view is not same as manually reconfigured
+ view
+ - Grouped annotation graph label has incorrect line colour
+ - Grouped annotation graph label display is corrupted for
+ lots of labels
|
@@ -381,13 +451,13 @@
specify which alignment a multi-structure view takes its
colours/correspondences from
Allow properties file location to be specified as URL
- Extend jalview project to preserve associations between
+ Extend Jalview project to preserve associations between
many alignment views and a single Jmol display
- Store annotation row height in jalview project file
+ Store annotation row height in Jalview project file
Annotation row column label formatting attributes stored
in project file
Annotation row order for auto-calculated annotation rows
- preserved in jalview project file
+ preserved in Jalview project file
Visual progress indication when Jalview state is saved
using Desktop window menu
Visual indication that command line arguments are still
@@ -412,7 +482,7 @@
Drag to reorder annotation rows in annotation panel
'automaticScrolling' parameter
Allow sequences with partial ID string matches to be
- annotated from GFF/jalview features files
+ annotated from GFF/Jalview features files
Sequence logo annotation row in applet
Absolute paths relative to host server in applet
parameters are treated as such
@@ -432,7 +502,7 @@
sortBy method
Set of applet and application examples shipped with
documentation
- New example to demonstrate jalviewLite and Jmol
+ New example to demonstrate JalviewLite and Jmol
javascript message exchange
General
@@ -441,7 +511,7 @@
multiple alignments
Option to automatically sort alignment with new tree
User configurable link to enable redirects to a
- www.jalview.org mirror
+ www.Jalview.org mirror
Jmol colours option for Jmol displays
Configurable newline string when writing alignment and
other flat files
@@ -456,8 +526,8 @@
Restructured javascript and applet api documentation
Ant target to publish example html files with applet
archive
- Netbeans project for building jalview from source
- ant task to create online javadoc for jalview source
+ Netbeans project for building Jalview from source
+ ant task to create online javadoc for Jalview source
Application
@@ -481,8 +551,8 @@
- Visibility status of autocalculated annotation row not
preserved when project is loaded
- Annotation row height and visibility attributes not stored
- in jalview project
- - Tree bootstraps are not preserved when saved as a jalview
+ in Jalview project
+ - Tree bootstraps are not preserved when saved as a Jalview
project
- Envision2 workflow tooltips are corrupted
- Enabling show group conservation also enables colour by
@@ -494,12 +564,12 @@
- Alignment quality not updated after alignment annotation
row is hidden then shown
- Preserve colouring of structures coloured by sequences in
- pre jalview 2.7 projects
+ pre Jalview 2.7 projects
- Web service job parameter dialog is not laid out properly
- Web services menu not refreshed after 'reset
services' button is pressed in preferences
- - Annotation off by one in jalview v2_3 example project
+ - Annotation off by one in Jalview v2_3 example project
- Structures imported from file and saved in project get
name like jalview_pdb1234.txt when reloaded
- Jalview does not always retrieve progress of a JABAWS job
@@ -524,7 +594,7 @@
- Status bar not updated after finished searching and search
wraps around to first result
- StructureSelectionManager instance shared between several
- jalview applets causes race conditions and memory leaks
+ Jalview applets causes race conditions and memory leaks
- Hover tooltip and mouseover of position on structure not
sent from Jmol in applet
- Certain sequences of javascript method calls to applet API
@@ -579,7 +649,7 @@
- Modeller PIR IO broken - cannot correctly import a pir
- file emitted by jalview
+ file emitted by Jalview
- Existing feature settings transferred to new alignment
view created from cut'n'paste
- Improved test for mixed amino/nucleotide chains when
@@ -626,11 +696,11 @@
1.5
- Allow Jalview feature colour specification for GFF sequence
annotation files
- - New 'colour by label' keword in jalview feature file type
+
- New 'colour by label' keword in Jalview feature file type
colour specification
- New Jalview Desktop Groovy API method that allows a script
to check if it being run in an interactive session or in a batch
- operation from the jalview command line
+ operation from the Jalview command line
|
@@ -774,7 +844,7 @@
href="webServices/index.html#envision2">Envision2 Workflows
- Vamsas Capabilities
- - Improved VAMSAS synchronization (jalview archive used to
+
- Improved VAMSAS synchronization (Jalview archive used to
preserve views, structures, and tree display settings)
- Import of vamsas documents from disk or URL via command
line
| |